ImageJ reslice all lines of a tiff image sequence (film) without opening them

Question

I'm using ImageJ to create spatio-temporal films using the reslice function of ImageJ on a sequence of tiff images. I do the reslice on all the lines of my images (or only on an area of the images) and I do this over a whole movie (image sequence). Therefore I have a film for which each image is a spatio-temporal image for a line of the original image.

My problem is that the size of my images is very large and I have 2021 images in my film. Therefore even though I dedicate 14Gb of ram to ImageJ on my Macbook Pro (16Gb of ram total), it take a lot of time of computation and in the end ImageJ appears to be out of memory.

Is it possible to launch such a computation without opening (or at least displaying) all the images?

Thank you for your help,

Best,

Adrien

Answer 1

Well, at some point you need to open the images to read in the data - but it doesn't necessarily mean they have to be opened at the same time. You might experiment with the "Virtual Stack" option, but as I don't fully understand what you're actually creating this might not be an option in your case...

Just not displaying the images should be easy, just use a macro and enable the so-called "Batch Mode". An example is given in the Fiji wiki:

input = "/home/fiji/input/";
output = "/home/fiji/images/";

setBatchMode(true); 
list = getFileList(input);
for (i = 0; i < list.length; i++)
    action(input, output, list[i]);
setBatchMode(false);